airr-seq

Generation probability, diversity, and simulation for AIRR-seq TCR/BCR repertoires, from graph models of decomposed receptor sequences. Python, C-accelerated.

[UNDER DEVELOPMENT] Pipeline for mapping and annotating T- and B-cell receptor gene rearrangement sequences

TCRscape - a tool for simultaneous multimodal gene expression and clonotype analysis of single T-cells profiled via the BD Rhapsody system.

Extract TCR and BCR clonotypes from raw sequencing data. Alignment against germline gene databases, error correction, receptor assembly, and clonotype grouping — turning FASTQ into a quantified repertoire with full QC.

Quality control scripts for AIRR-seq data

Barbera van Schaik, Antoine van Kampen: ENCORE project for analysis for T-cell and B-cell repertoires

Explore and annotate your sequences interactively, lets you write rule-based annotations that tag sequences by any criteria you choose

Barbera van Schaik, Antoine van Kampen: REpertoire SEquence Data Analysis

Matches clonotypes between two V(D)J datasets — typically a deep bulk dataset and a smaller single-cell reference — so any property from the reference becomes available on the matched bulk clonotypes.

Immunogenomics benchmark + skillset for AI agents

Re-groups an existing V(D)J dataset by a definition you choose — any combination of V gene, J gene, and CDR3 sequence — picks a representative for each new group, and recalculates every abundance column by summing across the members.

Rodrigo Garcia Valiente: Visual artsy representation of B-cell clonal repertoires using R

This repository contains bioinformatics workflows and Jupyter notebooks developed by the Molecular Virology and Vaccines Team (MVVT) for adaptive immune receptor repertoire sequencing (AIRR-seq) data. The workflows support B-cell receptor (BCR) repertoire analysis from bulk and single-cell sequencing data.

Calculates V and J gene segment usage frequencies across samples, plus their pairwise combinations, revealing the germline biases that antigen exposure, vaccination, and disease leave behind.

Data source tool for connecting a Galaxy instance to the immunological data bank iReceptor Plus Gateway.

Dasha Balashova, Antoine van Kampen, Barbera van Schaik: BCRCF

Compare repertoire diversity fairly across samples sequenced to different depths. Subsamples each library at a series of depths and plots how many unique sequences appear, producing rarefaction curves whose shape tells you whether you have captured a library's diversity or only scratched it.

Imports V(D)J data from various formats, including MiXCR, immunoSeq, AiRR and more (bulk or single-cell) and normalizes them into one standard clonotype dataset that every downstream